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Pyrosomes represent a group of marine holozooplankton. They do not exist as individual entities but as intricate colonies comprising numerous zooids, well-known for their bioluminescent properties. Pyrosomes inhabit most oceanic waters spanning tropical to temperate regions. They serve as significant consumers of phytoplankton, playing a crucial role in transport of organic carbon and sedimentation of organic matter debris. Nonetheless, the knowledge about this group remains limited, particularly concerning genomic and gene aspects. To further investigate the pyrosome at the molecular level, we used Pyrosoma atlanticum, which is the best known of pyrosome, for investigation in this study. We performed PacBio Iso-Seq and Illumina RNA-seq to generate high-quality and full-length transcript data from P. atlanticum. The systematic gene functional annotation was performed by integrated data. The full-length transcriptome produced in this study represents the inaugural dataset of transcriptome within the class Thaliacea, serving as a reference for future investigations. Additionally, as a stem group for chordates, the information of pyrosomes can provide a valuable research foundation for the evolution of vertebrates. [ABSTRACT FROM AUTHOR]

Onecut/Hnf6 (Oc) genes play an important role in the proper formation of retinal cells in vertebrates, in particular horizontal, retinal ganglion and amacrine cells. However, it is not fully known how the unique and combined action of multiple Oc gene copies leads to the induction and differentiation of specific retinal cell types. To gain new insights on how Oc genes influence retina formation, we have examined the developmental role of oc1, oc2 and oc-like genes during eye formation in the non-mammalian vertebrate zebrafish Danio rerio. By using single and multiple morpholino knockdown of three zebrafish Oc genes we provide evidence for the independent and redundant role of each gene in the formation of photoreceptors and other retinal tissues. Through comparison of Oc genetic pathways in photoreceptor differentiation among chordates we demonstrate their mechanism of action through a series of conserved target genes involved in neural transmission. [ABSTRACT FROM AUTHOR]

We assembled and annotated the complete mitochondrial genomes of Lycalopex vetulus (hoary fox), Cerdocyon thous (bush dog), Tayassu pecari (white-lipped peccary), and Tadarida brasiliensis (Brazilian free-tailed bat). The mitogenomes exhibited typical vertebrate structures, containing 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and a D-loop region. Phylogenetic reconstruction using the 13 protein-coding genes revealed robust relationships among species within Carnivora, Chiroptera, and Artiodactyla, corroborating previous studies. Secondary structure analysis of tRNAs and ribosomal genes showed slight variations among species of the same order. This research highlights the importance of mitochondrial genomics in understanding the evolutionary relationships and genetic diversity of Cerrado mammals, contributing to conservation efforts for this unique ecosystem. [ABSTRACT FROM AUTHOR]

Introns are highly prevalent in most eukaryotic genomes. Despite the accumulating evidence for benefits conferred by the possession of introns, their specific roles and functions, as well as the processes shaping their evolution, are still only partially understood. Here, we explore the evolution of the eukaryotic intron–exon gene structure by focusing on several key features such as the intron length, the number of introns, and the intron-to-exon length ratio in protein-coding genes. We utilize whole-genome data from 590 species covering the main eukaryotic taxonomic groups and analyze them within a statistical phylogenetic framework. We found that the basic gene structure differs markedly among the main eukaryotic groups, with animals, and particularly chordates, displaying intron-rich genes, compared with plants and fungi. Reconstruction of gene structure evolution suggests that these differences evolved prior to the divergence of the main phyla and have remained mostly conserved within groups. We revisit the previously reported association between the genome size and the mean intron length and report that this association differs considerably among phyla. Analyzing a large and diverse dataset of species with whole-genome information while applying advanced modeling techniques allowed us to obtain a global evolutionary perspective. Our findings may indicate that introns play different molecular and evolutionary roles in different organisms. [ABSTRACT FROM AUTHOR]

The evolution of the distinct chordate body plan has intrigued scientists for over 170 years. Modern genomics and transcriptomics have allowed the elucidation of the developmental gene regulatory networks (GRNs) underlying the developmental programs for particular tissues and body axes in invertebrates and vertebrates. This has been most revealing in the Deuterostomia, the superphylum in which chordates evolved. The time was ripe to gather those working on deuterostome developmental GRNs to revisit the development and evolution of chordates and discuss the evolution of this unique body plan at the SICB 2024 meetings in Seattle, WA, USA. It has been several years since the genomes of the major deuterostome clades have been sequenced—echinoderms, hemichordates, tunicates, lancelets, and vertebrates. Genomic analyses have shown that lancelets have a genome and body plan that closely resemble the vertebrates, although phylogenomic analyses suggest that the tunicates are the sister group of the vertebrates. The evolution of the sessile and sometimes colonial adult tunicates was likely from a motile, lancelet-like ancestor. Scientists from all over the world converged at the SICB meetings in Seattle to discuss the current ideas of how chordates evolved. Some common mechanisms and themes emerged and are captured in this ICB volume on Chordate Origins, Evolution, and Development. [ABSTRACT FROM AUTHOR]

The evolutionary origins of chordates and their diversification into the three major subphyla of tunicates, vertebrates, and cephalochordates pose myriad questions about the genetic and developmental mechanisms underlying this radiation. Studies in non-vertebrate chordates have refined our model of what the ancestral chordate may have looked like, and have revealed the pre-vertebrate origins of key cellular and developmental traits. Work in the major tunicate laboratory model Ciona has benefitted greatly from the emergence of CRISPR/Cas9 techniques for targeted gene disruption. Here we review some of the important findings made possible by CRISPR in Ciona , and present our latest protocols and recommended practices for plasmid-based, tissue-specific CRISPR/Cas9-mediated mutagenesis. [ABSTRACT FROM AUTHOR]

In polymorphic organisms, a single genome is deployed to program numerous, morphologically distinct body plans within a colony. This complex life history trait has evolved independently within a limited subset of animal taxa. Reconstructing the underlying genetic, cellular, and developmental changes that drove the emergence of polymorphic colonies represents a promising avenue for exploring diversifying selection and resulting impacts on developmental gene regulatory networks. Doliolids are the only polymorphic chordate, deploying a single genome to program distinct morphs specialized for locomotion, feeding, asexual, or sexual reproduction. In this review, we provide a detailed summary of doliolid anatomy, development, taxonomy, ecology, life history, and the cellular basis for doliolid polymorphism. In order to frame the potential evolutionary and developmental insights that could be gained by studying doliolids, we provide a broader overview of polymorphism. We then discuss how comparative studies of polymorphic cnidarians have begun to illuminate the genetic basis of this unusual and complex life history strategy. We then provide a summary of life history divergence in the chordates, particularly among doliolids and their polymorphic cousins, the salps and pyrosomes. [ABSTRACT FROM AUTHOR]

Metameric somites are a novel character of chordates with unclear evolutionary origins. In the early branching chordate amphioxus, anterior somites are derived from the paraxial mesodermal cells that bud off the archenteron (i.e. enterocoely) at the end of gastrulation. Development of the anterior somites requires fibroblast growth factor (FGF) signaling, and distinct somite compartments express orthologs of vertebrate nonaxial mesodermal markers. Thus, it has been proposed that the amphioxus anterior somites are homologous to the vertebrate head mesoderm, paraxial mesoderm, and lateral plate mesoderm. To trace the evolutionary origin of somites, it is essential to study the chordates' closest sister group, Ambulacraria, which includes hemichordates and echinoderms. The anterior coeloms of hemichordate and sea urchin embryos (respectively called protocoel and coelomic pouches) are also formed by enterocoely and require FGF signals for specification and/or differentiation. In this study, we applied RNA-seq to comprehensively screen for regulatory genes associated with the mesoderm-derived protocoel of the hemichordate Ptychodera flava. We also used a candidate gene approach to identify P. flava orthologs of chordate somite markers. In situ hybridization results showed that many of these candidate genes are expressed in distinct or overlapping regions of the protocoel, which indicates that molecular compartments exist in the hemichordate anterior coelom. Given that the hemichordate protocoel and amphioxus anterior somites share a similar ontogenic process (enterocoely), induction signal (FGF), and characteristic expression of orthologous genes, we propose that these two anterior coeloms are indeed homologous. In the lineage leading to the emergence of chordates, somites likely evolved from enterocoelic, FGF-dependent, and molecularly compartmentalized anterior coeloms of the deuterostome last common ancestor. [ABSTRACT FROM AUTHOR]

Vertebrates and tunicates are sister groups that share a common fusogenic factor, Myomaker (Mymk), that drives myoblast fusion and muscle multinucleation. Yet they are divergent in when and where they express Mymk. In vertebrates, all developing skeletal muscles express Mymk and are obligately multinucleated. In tunicates, Mymk is expressed only in post-metamorphic multinucleated muscles, but is absent from mononucleated larval muscles. In this study, we demonstrate that cis-regulatory sequence differences in the promoter region of Mymk underlie the different spatiotemporal patterns of its transcriptional activation in tunicates and vertebrates. Although in vertebrates myogenic regulatory factors (MRFs) such as MyoD1 alone are required and sufficient for Mymk transcription in all skeletal muscles, we show that transcription of Mymk in post-metamorphic muscles of the tunicate Ciona requires the combinatorial activity of MRF, MyoD and Early B-cell Factor (Ebf). This macroevolutionary difference appears to be encoded in cis, likely due to the presence of a putative Ebf-binding site adjacent to predicted MRF binding sites in the Ciona Mymk promoter. We further discuss how Mymk and myoblast fusion might have been regulated in the last common ancestor of tunicates and vertebrates, for which we propose two models. [ABSTRACT FROM AUTHOR]

ABSTRACT Plants and animals are often adorned with potentially conspicuous colours (e.g. red, yellow, orange, blue, purple). These include the dazzling colours of fruits and flowers, the brilliant warning colours of frogs, snakes, and invertebrates, and the spectacular sexually selected colours of insects, fish, birds, and lizards. Such signals are often thought to utilize pre‐existing sensitivities in the receiver's visual systems. This raises the question: what was the initial function of conspicuous colouration and colour vision? Here, we review the origins of colour vision, fruit, flowers, and aposematic and sexually selected colouration. We find that aposematic colouration is widely distributed across animals but relatively young, evolving only in the last ~150 million years (Myr). Sexually selected colouration in animals appears confined to arthropods and chordates, and is also relatively young (generally <100 Myr). Colourful flowers likely evolved ~200 million years ago (Mya), whereas colourful fruits/seeds likely evolved ~300 Mya. Colour vision (sensu lato) appears to be substantially older, and likely originated ~400–500 Mya in both arthropods and chordates. Thus, colour vision may have evolved long before extant lineages with fruit, flowers, aposematism, and sexual colour signals. We also find that there appears to have been an explosion of colour within the last ~100 Myr, including >200 origins of aposematic colouration across nine animal phyla and >100 origins of sexually selected colouration among arthropods and chordates. [ABSTRACT FROM AUTHOR]

Different frequencies amongst codons that encode the same amino acid (i.e. synonymous codons) have been observed in multiple species. Studies focused on uncovering the forces that drive such codon usage showed that a combined effect of mutational biases and translational selection works to produce different frequencies of synonymous codons. However, only few have been able to measure and distinguish between these forces that may leave similar traces on the coding regions. Here, we have developed a codon model that allows the disentangling of mutation, selection on amino acids and synonymous codons, and GC-biased gene conversion (gBGC) which we employed on an extensive dataset of 415 chordates and 191 arthropods. We found that chordates need 15 more synonymous codon categories than arthropods to explain the empirical codon frequencies, which suggests that the extent of codon usage can vary greatly between animal phyla. Moreover, methylation at CpG sites seems to partially explain these patterns of codon usage in chordates but not in arthropods. Despite the differences between the two phyla, our findings demonstrate that in both, GC-rich codons are disfavored when mutations are GC-biased, and the opposite is true when mutations are AT-biased. This indicates that selection on the genomic coding regions might act primarily to stabilize its GC/AT content on a genome-wide level. Our study shows that the degree of synonymous codon usage varies considerably among animals, but is likely governed by a common underlying dynamic. [ABSTRACT FROM AUTHOR]

An unidentified colonial ascidian called gaikotsu-panda-hoya in Japanese, literally meaning ‘skeleton panda ascidian,’ has been attracting SCUBA divers’ attention for the past few years since its strange appearance was introduced on the Internet by a diving shop in Kumejima Island, Japan. To confirm the taxonomic status of this species, fresh samples were collected from a diving point off the coast of Kumejima Island. Our morphological examination revealed that they represent a new species, herein described as Clavelina ossipandae sp. nov., which can be distinguished from 44 congeners in the genus Clavelina Savigny, 1816 by the combination of the following seven characteristics: i) colony consisting of completely free zooids, ii) zooids up to 20 mm in length, iii) in the living state, zooids transparent, with laterally elongated white patch between oral and atrial siphons, as well as four black markings, one between siphons, one mid-dorsally, and the other two situated laterally in a pair on the anterior part of the body, iv) transverse vessels white, v) endostyle black, vi) 10–14 stigmatal rows, and vii) two longitudinal muscular bands running from the abdomen to the endostyle on each side. Partial sequences (810 bp) of the cytochrome c oxidase subunit I gene from the holotype and one of the paratypes differed at 10 sites from each other (1.26% K2P distance) but were the same when translated into amino acids. A phylogenetic tree supported that this species is included in the genus Clavelina.

Hemichordata has always played a central role in evolutionary studies of Chordata due to their close phylogenetic affinity and shared morphological characteristics. Hemichordates had no meiofaunal representatives until the surprising discovery of a microscopic, paedomorphic enteropneust Meioglossus psammophilus (Harrimaniidae, Hemichordata) from the Caribbean in 2012. No additional species have been described since, questioning the broader distribution and significance of this genus. However, being less than a millimeter long and superficially resembling an early juvenile acorn worm, Meioglossus may easily be overlooked in both macrofauna and meiofauna surveys. We here present the discovery of 11 additional populations of Meioglossus from shallow subtropical and tropical coralline sands of the Caribbean Sea, Red Sea, Indian Ocean, and East China Sea. These geographically separated populations show identical morphology but differ genetically. Our phylogenetic reconstructions include four gene markers and support the monophyly of Meioglossus. Species delineation analyses revealed eight new cryptic species, which we herein describe using DNA taxonomy. This study reveals a broad circumtropical distribution, supporting the validity and ecological importance of this enigmatic meiobenthic genus. The high cryptic diversity and apparent morphological stasis of Meioglossus may exemplify a potentially common evolutionary 'dead-end' scenario, where groups with highly miniaturized and simplified body plan lose their ability to diversify morphologically. [ABSTRACT FROM AUTHOR]

Investigating ventricular diastolic properties is crucial for understanding the physiological cardiac functions in organisms and unraveling the pathological mechanisms of cardiovascular disorders. Ventricular stiffness, a fundamental parameter that defines ventricular diastolic functions in chordates, is typically analyzed using the end‐diastolic pressure–volume relationship (EDPVR). However, comparing ventricular stiffness accurately across chambers of varying maximum volume capacities has been a long‐standing challenge. As one of the solutions to this problem, we propose calculating a relative ventricular stiffness index by applying an exponential approximation formula to the EDPVR plot data of the relationship between ventricular pressure and values of normalized ventricular volume by the ventricular weight. This article reviews the potential, utility, and limitations of using normalized EDPVR analysis in recent studies. Herein, we measured and ranked ventricular stiffness in differently sized and shaped chambers using ex vivo ventricular pressure‐volume analysis data from four animals: Wistar rats, red‐eared slider turtles, masu salmon, and cherry salmon. Furthermore, we have discussed the mechanical effects of intracellular and extracellular viscoelastic components, Titin (Connectin) filaments, collagens, physiological sarcomere length, and other factors that govern ventricular stiffness. Our review provides insights into the comparison of ventricular stiffness in different‐sized ventricles between heterologous and homologous species, including non‐model organisms. [ABSTRACT FROM AUTHOR]

The Myc family of proto-oncogenes is a key node for the signal transduction of external pro-proliferative signals to the cellular processes required for development, tissue homoeostasis maintenance, and regeneration across evolution. The tight regulation of Myc synthesis and activity is essential for restricting its oncogenic potential. In this review, we highlight the central role that Myc plays in regeneration across the animal kingdom (from Cnidaria to echinoderms to Chordata) and how Myc could be employed to unlock the regenerative potential of non-regenerative tissues in humans for therapeutic purposes. Mastering the fine balance of harnessing the ability of Myc to promote transcription without triggering oncogenesis may open the door to many exciting opportunities for therapeutic development across a wide array of diseases. [ABSTRACT FROM AUTHOR]

Hypertension, a major health concern linked to heart disease and premature mortality, has prompted a search for alternative treatments due to side effects of existing medications. Sustainable harvesting of low-trophic marine organisms not only enhances food security but also provides a variety of bioactive molecules, including peptides. Despite comprising only a fraction of active natural compounds, peptides are ideal for drug development due to their size, stability, and resistance to degradation. Our review evaluates the anti-hypertensive properties of peptides and proteins derived from selected marine invertebrate phyla, examining the various methodologies used and their application in pharmaceuticals, supplements, and functional food. A considerable body of research exists on the anti-hypertensive effects of certain marine invertebrates, yet many species remain unexamined. The array of assessments methods, particularly for ACE inhibition, complicates the comparison of results. The dominance of in vitro and animal in vivo studies indicates a need for more clinical research in order to transition peptides into pharmaceuticals. Our findings lay the groundwork for further exploration of these promising marine invertebrates, emphasizing the need to balance scientific discovery and marine conservation for sustainable resource use. [ABSTRACT FROM AUTHOR]

The pharyngeal endoderm, an innovation of deuterostome ancestors, contributes to pharyngeal development by influencing the patterning and differentiation of pharyngeal structures in vertebrates; however, the evolutionary origin of the pharyngeal organs in vertebrates is largely unknown. The endostyle, a distinct pharyngeal organ exclusively present in basal chordates, represents a good model for understanding pharyngeal organ origins. Using Stereo-seq and single-cell RNA sequencing, we constructed aspatially resolved single-cell atlas for the endostyle of the ascidian Styela clava. We determined the cell composition of the hemolymphoid region, which illuminates a mixed ancestral structure for the blood and lymphoid system. In addition, we discovered a cluster of hair cell-like cells in zone 3, which has transcriptomic similarity with the hair cells of the vertebrate acoustico-lateralis system. These findings reshape our understanding of the pharynx of the basal chordate and provide insights into the evolutionary origin of multiplexed pharyngeal organs. [ABSTRACT FROM AUTHOR]

Attempts to explain the origin and diversification of vertebrates have commonly invoked the evolution of feeding ecology, contrasting the passive suspension feeding of invertebrate chordates and larval lampreys with active predation in living jawed vertebrates. Of the extinct jawless vertebrates that phylogenetically intercalate these living groups, the feeding apparatus is well-preserved only in the early diverging stem-gnathostome heterostracans. However, its anatomy remains poorly understood. Here, we use X-ray microtomography to characterize the feeding apparatus of the pteraspid heterostracan Rhinopteraspis dunensis (Roemer, 1855). The apparatus is composed of 13 plates arranged approximately bilaterally, most of which articulate from the postoral plate. Our reconstruction shows that the oral plates were capable of rotating around the transverse axis, but likely with limited movement. It also suggests the nasohypophyseal organs opened internally, into the pharynx. The functional morphology of the apparatus in Rhinopteraspis precludes all proposed interpretations of feeding except for suspension/deposit feeding and we interpret the apparatus as having served primarily to moderate the oral gape. This is consistent with evidence that at least some early jawless gnathostomes were suspension feeders and runs contrary to macroecological scenarios that envisage early vertebrate evolution as characterized by a directional trend towards increasingly active food acquisition. [ABSTRACT FROM AUTHOR]

Deepor Beel, located in the state of Assam in India, is a Wetland of International Importance with a Wildlife Sanctuary and is the only RAMSAR site in the state. Though of invaluable ecological significance, the wetland is facing anthropogenic stressors, leading to rapid degradation of ecological health. In December 2022, surface water was collected from six stations of Deepor Beel to elucidate biological communities using the eDNA approach. At the time of sampling, in-situ environmental parameters were measured in triplicates. The dissolved nutrients and concentrations of metals and metalloids were estimated using UV–Vis Spectrophotometry and ICP-MS approaches respectively. The study revealed a high concentration of dissolved nitrate in the surface water. High-throughput sequencing using Nanopore sequencing chemistry in a MinION platform indicated the overwhelming abundance of Moraxellaceae (Prokaryotes) and Eumetazoa (Eukaryotes). The abundance of Cyprinidae were also encountered in the studied wetland reflecting the biodiversity of fish populations. High nitrate along with elucidated microbial signals are crucial to designate ecological health status of Deeper Beel. This study is aimed at generating baseline information to aid long-term monitoring and restoration of the Deepor Beel as well as the first comprehensive assessment of a RAMSAR Site located in northeast of India.

Simple Summary: Anticancer peptides are short aminoacidic chains, which display selective cytotoxicity mostly against tumor, but not healthy, cells through interference with intracellular biological events. The marine environment features an ever-growing level of biodiversity and, therefore, seas and oceans are indeed poorly exploited mines in terms of natural products of biomedical interest. Adaptation processes to extreme and competitive environmental conditions led marine species to produce unique metabolites, which have found broad use for various applications in healthcare management, due to their anticancer, anti-angiogenic, anti-inflammatory and regeneration abilities. The aim of this review is to pick and list selected studies that report on the isolation of marine animal-derived peptides and the identification of their anticancer activity in in vitro cultures of cancer cells. Anticancer peptides are short and structurally heterogeneous aminoacidic chains, which display selective cytotoxicity mostly against tumor cells, but not healthy cells, based on their different cell surface properties. Their anti-tumoral activity is carried out through interference with intracellular homeostasis, such as plasmalemma integrity, cell cycle control, enzymatic activities and mitochondrial functions, ultimately acting as angiogenesis-, drug resistance- and metastasis-inhibiting agents, immune stimulators, differentiation inducers and necrosis or extrinsic/intrinsic apoptosis promoters. The marine environment features an ever-growing level of biodiversity, and seas and oceans are poorly exploited mines in terms of natural products of biomedical interest. Adaptation processes to extreme and competitive environmental conditions led marine species to produce unique metabolites as a chemical strategy to allow inter-individual signalization and ensure survival against predators, infectious agents or UV radiation. These natural metabolites have found broad use in various applications in healthcare management, due to their anticancer, anti-angiogenic, anti-inflammatory and regeneration abilities. The aim of this review is to pick selected studies that report on the isolation of marine animal-derived peptides and the identification of their anticancer activity in in vitro cultures of cancer cells, and list them with respect to the taxonomical hierarchy of the source organism. [ABSTRACT FROM AUTHOR]

Fimbrora Monniot & Monniot, 1991, a macrophagous ascidian genus within the family Ascidiidae Adams & Adams, 1858, is currently monotypic, represented by F. calsubia Monniot & Monniot, 1991, a species previously recorded from the bottom of the South Pacific at depths of 1000–1860 m. The taxonomic status of Fimbrora has remained ambiguous because characteristics in its branchial papillae and neural-gland opening are incompletely known in previous studies, while these traits are essential for distinguishing other ascidiid genera. So far, no nucleotide sequence representing F. calsubia is available. In this study, we collected a single specimen of F. calsubia at a depth of 2027 m, about 400 km off the Pacific coast of Honshu, Japan. This is the deepest record, as well as the first report from the North Pacific, for the species. Our examination indicates that Fimbrora is morphologically similar to another ascidiid genus, Psammascidia Monniot, 1962, by having only secondary branchial papillae in the pharynx. Our phylogenetic analysis, based on the 18S ribosomal RNA and cytochrome c oxidase subunit I genes, along with those of 27 ascidian species available in public databases, showed that F. calsubia was more closely related to Ascidia zara Oka, 1935, Phallusia fumigata (Grube, 1864) and Phallusia mammilata (Cuvier, 1815) than to Ascidia ceratodes (Huntsman, 1912), Ascidiella aspersa (Müller, 1776) and Ascidiella scabra (Müller, 1776). Our results also indicated that acquisitions of macrophagous feeding by deep-sea members happened independently at least three times in the evolutionary history of the entire Ascidiacea. [ABSTRACT FROM AUTHOR]

Ascidians are rapidly emerging biofouling organisms that generally occur on the natural and artificial substratum of the marine environment. However, very few studies have been reported on their species diversity and distribution patterns. This present investigation focuses on the seasonal impact on ascidians diversity. The distributions of ascidians were recorded by the collection of samples in six sampling stations from Andaman and Nicobar Islands. A total of 43 species of ascidians (32 colonial, 11 solitary) were recorded and most of the species are under the Didemnidae family. Various diversity indexes were utilized to examine the diversity, richness and evenness of species and to look at the assorted variety among tests and their likeness regarding species composition. The greatest (3.227) individuals were observed during summer season in Pigeon Island and the lowest (2.063) number of species were recorded during the monsoon season in Haddowharf harbour. The Margalef richness (d) fluctuated between in the range of 2.033 and 5.53 during the monsoon in Haddowharf harbour and Carbyns Cove beach in summer seasons. The Pielou's evenness record (J′) changed from 0.7409 to 0.9713. Diversity indexes were recorded as followed the order of 0.9642, 0.9552, 0.9482 and 0.9292 at Carbyns Cove shoreline, Burmanella, Pigeon Island and Campbell Bay individually during summer season. Present findings in the cluster examination uncovered that the species at various stations have framed four gatherings. Most elevated species rates were spread in summer. Field observation shows that species distribution is able to tolerate temperature ranges of 26.9–30.3°C and salinity of 32.1–34.64 ppt. Occasional examples of space occupation by colonial ascidians corresponded with seasonal changes in seawater temperature and salinity. [ABSTRACT FROM AUTHOR]

In this study, mitochondrial genomes (mitogenomes) of seven cichlid species (Lamprologus kungweensis, L. meleagris, L. ornatipinnis, Neolamprologus brevis, N. caudopunctatus, N. leleupi, and N. similis) are characterized for the first time. The newly sequenced mitogenomes contained 37 typical genes [13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs) and 22 transfer RNA genes (tRNAs)]. The mitogenomes were 16,562 ~ 16,587 bp in length with an A+T composition of 52.1~58.8%. The cichlid mitogenomes had a comparable nucleotide composition, A+T content was higher than the G+C content. The AT-skews of most mitogenomes were inconspicuously positive and the GC-skews were negative, indicating higher occurrences of C than G. Most PCGs started with the conventional start codon, ATN. There was no essential difference in the codon usage patterns of these seven species. Using Ka/Ks, we found the fastest-evolving gene were atp8. But the results of p-distance indicated that the fastest-evolving gene was nad6. Phylogenetic analysis revealed that L. meleagris did not cluster with Lamprologus species, but with species from the genus Neolamprologus. The novel information obtained about these mitogenomes will contribute to elucidating the complex relationships among cichlid species. [ABSTRACT FROM AUTHOR]

We identified 23 and 20 cytoplasmic IF (cIF) genes in the two Branchiostoma belcheri and Branchiostoma lanceolatum cephalochordates, respectively. Combining these results with earlier data on the related Branchiostoma floridae, the following conclusions can be drawn. First, the Branchiostoma N4 protein with a long lamin-like coil 1B segment is the only protostomic-type cIF found so far in any analysed chordate or vertebrate organism. Second, Branchiostoma is the only organism known so far containing both the long protostomic- and the short chordate-prototypes of cIFs. This finding provides so far missing molecular evidence for the phylogenetic transition between the protostomic- and the chordate-type IF sequences at the base of the cephalochordates and vertebrates. Third, this finding also brings some support for another hypothesis, that the long protostomic-type cIF is subjected to evolutionary constraints in order to preclude inappropriate interactions with lamin and that the latter complexes might be prevented by a several heptad-long rod deletion, which released the selective constraints on it and promoted, at least in part, its expansion in nematodes, cephalochordates, and in vertebrates. Finally, here-presented data confirmed our previous results that cephalochordates do not have any vertebrate type III or type IV IF homolog. [ABSTRACT FROM AUTHOR]

Hemichordates are close relatives of chordates. Their nervous system patterning is chordate-like, but their neural architecture remains unexplored. A new study in PLOS Biology reveals an unexpected neuroanatomical complexity in these animals, also informing chordate origins. Hemichordates, close relatives of chordates, have a nervous system that is chordate-like in its patterning but their neural architecture remains unexplored. This Primer explores a new study in PLOS Biology that reveals an unexpected neuroanatomical complexity in these animals. [ABSTRACT FROM AUTHOR]

Cephalochordates and tunicates represent the only two groups of invertebrate chordates, and extant cephalochordates - commonly known as amphioxus or lancelets - are considered the best proxy for the chordate ancestor, from which they split around 520 million years ago. Amphioxus has been an important organism in the fields of zoology and embryology since the 18th century, and the morphological and genomic simplicity of cephalochordates (compared to vertebrates) makes amphioxus an attractive model for studying chordate biology at the cellular and molecular levels. Here we describe the life cycle of amphioxus, and discuss the natural histories and habitats of the different species of amphioxus. We also describe their use as laboratory animal models, and discuss the techniques that have been developed to study different aspects of amphioxus. [ABSTRACT FROM AUTHOR]

The lowland region of Sumatra Barat has received little attention in previous biodiversity studies. Past studies have mainly focused on highland habitat and conservation areas. However, many populations of Cyrtodactylus in the lowland habitats of Sumatra Barat were not correctly identified. A phylogenetic tree based on the NADH dehydrogenase subunit 2 (ND2) gene showed that the lowland Sumatran population is the sister group of the Malaysian lowland species, C. semenanjungensis, together nesting within the agamensis group. The genetic divergence within the Sumatra Barat population is 0-4.2% and 18.3-20% to C. semenanjungensis. Further examination of morphological characters revealed that they differed from the sister clade and other Sumatran Cyrtodactylus members by a unique combination of characters such as absence of tubercle on brachium, presence of tubercle on ventrolateral fold, 32-41 paravertebral tubercles, 38-46 ventral scales, enlarged femoral scales, presence of precloacofemoral pores and 22-23 subdigital lamellae under fourth toe. Based on the morphological and molecular evidence, the lowland Sumatran population is herein described as a new species, increasing the number of species in Sumatra to seven. More comprehensive and intensive sampling efforts would most likely yield further discoveries in the group of Sumatran Cyrtodactylus in the near future. [ABSTRACT FROM AUTHOR]

Nitric oxide (NO) is a key signaling molecule in almost all organisms and is active in a variety of physiological and pathological processes. Our understanding of the peculiarities and functions of this simple gas has increased considerably by extending studies to non-mammal vertebrates and invertebrates. In this review, we report the nitric oxide synthase (Nos) genes so far characterized in chordates and provide an extensive, detailed, and comparative analysis of the function of NO in the aquatic chordates tunicates, cephalochordates, teleost fishes, and amphibians. This comprehensive set of data adds new elements to our understanding of Nos evolution, from the single gene commonly found in invertebrates to the three genes present in vertebrates. [ABSTRACT FROM AUTHOR]

Among the six species of Cyrtodactylus occurring in Sumatra, two species were described based on non-Sumatran type series, C. consobrinus and C. quadrivirgatus. The latter species was described originally from Thailand thus the wider distribution in Sumatra should be clarified taxonomically. Cyrtodactylus quadrivirgatus from Sumatra Barat was examined using both morphology and the Natrium Dehydrogenase Subunit 2 (ND2) gene to clarify its taxonomic status and phylogenetic placement. It was found that these specimens form a sister clade to all other species of the sworderi group from Peninsular Malaysia and the genetic distance ranges from 20-24.3%. This subset is herein described as a new species. The new species is readily distinguished from C. quadrivirgatus and other Sumatran species by a combination of characters: small size SVL 37.5-53.78 mm; longitudinal rows of dorsal tubercles 16-19; paravertebral tubercles 31-41; ventral scales 32-43; 24-49 enlarged precloacal and femoral scales; precloacal pores rarely present; no precloacal depression; two postcloacal tubercles on each side; 14-19 subdigital lamellae on forth toe; 9-15 supralabial scales; 9-12 infralabial scales; three or four internasal scales; and 3-6 gular scales that border the first pair of postmental scales. This work underscores the importance of clarifying widely distributed species for taxonomic validation. [ABSTRACT FROM AUTHOR]

Gastrulation is a critical event whose molecular mechanisms are thought to be conserved among vertebrates. However, the morphological movement during gastrulation appears to be divergent across species, making it difficult to discuss the evolution of the process. Previously, we proposed a novel amphibian gastrulation model, the "subduction and zippering (S&Z) model". In this model, the organizer and the prospective neuroectoderm are originally localized in the blastula's blastocoel roof, and these embryonic regions move downward to make physical contact of their inner surfaces with each other at the dorsal marginal zone. The developmental stage when contact between the head organizer and the anterior-most neuroectoderm is established is called "anterior contact establishment (ACE)." After ACE, the A-P body axis elongates posteriorly. According to this model, the body axis is derived from limited regions of the dorsal marginal zone at ACE. To investigate this possibility, we conducted stepwise tissue deletions using Xenopus laevis embryos and revealed that the dorsal one-third of the marginal zone had the ability to form the complete dorsal structure by itself. Furthermore, a blastocoel roof explant of the blastula, which should contain the organizer and the prospective neuroectoderm in the S&Z model, autonomously underwent gastrulation and formed the complete dorsal structure. Collectively, these results are consistent with the S&Z gastrulation model and identify the embryonic region sufficient for construction of the complete dorsal structure. Finally, by comparing amphibian gastrulation to gastrulation of protochordates and amniotes, we discuss the gastrulation movement evolutionarily conserved among chordates. [ABSTRACT FROM AUTHOR]

The vertebrate head skeleton has evolved a myriad of forms since their divergence from invertebrate chordates. The connection between novel gene expression and cell types is therefore of importance in this process. The transformation of the jawed vertebrate (gnathostome) head skeleton from oral cirri to jointed jaw elements required a diversity of cartilages as well as changes in the patterning of these tissues. Although lampreys are a sister clade to gnathostomes, they display skeletal diversity with distinct gene expression and histologies, a useful model for addressing joint evolution. Specifically, the lamprey tissue known as mucocartilage has noted similarities with the jointed elements of the mandibular arch in jawed vertebrates. We thus asked whether the cells in lamprey mucocartilage and gnathostome joint tissue could be considered homologous. To do this, we characterized new genes that are involved in gnathostome joint formation and characterized the histochemical properties of lamprey skeletal types. We find that most of these genes are minimally found in mucocartilage and are likely later innovations, but we do identify new activity for gdf5/6/7b in both hyaline and mucocartilage, supporting its role as a chondrogenic regulator. Contrary to previous works, our histological assays do not find any perichondrial fibroblasts surrounding mucocartilage, suggesting that mucocartilage is non-skeletogenic tissue that is partially chondrified. Interestingly, we also identify new histochemical features of the lamprey otic capsule that diverge from normal hyaline. Paired with our new insights into lamprey mucocartilage, we propose a broader framework for skeletal evolution in which an ancestral soxD/E and gdf5/6/7 network directs mesenchyme along a spectrum of cartilage-like features. [ABSTRACT FROM AUTHOR]

The present contribution is chiefly a review, augmented by some new results on amphioxus and lamprey anatomy, that draws on paleontological and developmental data to suggest a scenario for cranial cartilage evolution in the phylum chordata. Consideration is given to the cartilage‐related tissues of invertebrate chordates (amphioxus and some fossil groups like vetulicolians) as well as in the two major divisions of the subphylum Vertebrata (namely, agnathans, and gnathostomes). In the invertebrate chordates, which can be considered plausible proxy ancestors of the vertebrates, only a viscerocranium is present, whereas a neurocranium is absent. For this situation, we examine how cartilage‐related tissues of this head region prefigure the cellular cartilage types in the vertebrates. We then focus on the vertebrate neurocranium, where cyclostomes evidently lack neural‐crest derived trabecular cartilage (although this point needs to be established more firmly). In the more complex gnathostome, several neural‐crest derived cartilage types are present: namely, the trabecular cartilages of the prechordal region and the parachordal cartilage the chordal region. In sum, we present an evolutionary framework for cranial cartilage evolution in chordates and suggest aspects of the subject that should profit from additional study. Research highlights: Developmental comparison of amphioxus, cyclostomes, and gnathostome cartilage properties provides the knowledge of key changes for the evolution of the vertebrate neurocranium. The trabecular cartilage, which is the key element for the gnathostome neurocranium, may have been derived from the ancient pharyngeal mesoderm. [ABSTRACT FROM AUTHOR]

The central nervous system (CNS) of chordates, including humans, develops as a hollow tube with ciliated walls containing cerebrospinal fluid. However, most of the animals inhabiting our planet do not use this design and rather build their centralized brains from non-epithelialized condensations of neurons called ganglia, with no traces of epithelialized tubes or liquid-containing cavities. The evolutionary origin of tube-type CNSs stays enigmatic, especially as non-epithelialized ganglionic-type nervous systems dominate the animal kingdom. Here, I discuss recent findings relevant to understanding the potential homologies and scenarios of the origin, histology and anatomy of the chordate neural tube. The nerve cords of other deuterostomes might relate to the chordate neural tube at histological, developmental and cellular levels, including the presence of radial glia, layered stratification, retained epithelial features, morphogenesis via folding and formation of a lumen filled with liquid. Recent findings inspire a new view of hypothetical evolutionary scenarios explaining the tubular epithelialized structure of the CNS. One such idea suggests that early neural tubes were key for improved directional olfaction, which was facilitated by the liquid-containing internal cavity. The later separation of the olfactory portion of the tube led to the formation of the independent olfactory and posterior tubular CNS systems in vertebrates. According to an alternative hypothesis, the thick basiepithelial nerve cords could provide deuterostome ancestors with additional biomechanical support, which later improved by turning the basiepithelial cord into a tube filled with liquid — a hydraulic skeleton. In this review, Igor Adameyko examines the current literature and proposes hypotheses about the evolutionary origins of a tubular central nervous system in chordates. [ABSTRACT FROM AUTHOR]

Type IB topoisomerases relax the torsional stress associated with DNA metabolism in the nucleus and mitochondria and constitute important molecular targets of anticancer drugs. Vertebrates stand out among eukaryotes by having two Type IB topoisomerases acting specifically in the nucleus (TOP1) and mitochondria (TOP1MT). Despite their major importance, the origin and evolution of these paralogues remain unknown. Here, we examine the molecular evolutionary processes acting on both TOP1 and TOP1MT in Chordata, taking advantage of the increasing number of available genome sequences. We found that both TOP1 and TOP1MT evolved under strong purifying selection, as expected considering their essential biological functions. Critical active sites, including those associated with resistance to anticancer agents, were found particularly conserved. However, TOP1MT presented a higher rate of molecular evolution than TOP1, possibly related with its specialized activity on the mitochondrial genome and a less critical role in cells. We could place the duplication event that originated the TOP1 and TOP1MT paralogues early in the radiation of vertebrates, most likely associated with the first round of vertebrate tetraploidization (1R). Moreover, our data suggest that cyclostomes present a specialized mitochondrial Type IB topoisomerase. Interestingly, we identified two missense mutations replacing amino acids in the Linker region of TOP1MT in Neanderthals, which appears as a rare event when comparing the genome of both species. In conclusion, TOP1 and TOP1MT differ in their rates of evolution, and their evolutionary histories allowed us to better understand the evolution of chordates. [ABSTRACT FROM AUTHOR]

Amphioxus species are considered living fossils and are important in the evolutionary study of chordates and vertebrates. To explore viral homologous sequences, a high-quality annotated genome of the Beihai amphioxus (Branchiostoma belcheri beihai) was examined using virus sequence queries. In this study, 347 homologous fragments (HFs) of viruses were identified in the genome of B. belcheri beihai, of which most were observed on 21 genome assembly scaffolds. HFs were preferentially located within protein-coding genes, particularly in their CDS regions and promoters. A range of amphioxus genes with a high frequency of HFs is proposed, including histone-related genes that are homologous to the Histone or Histone H2B domains of viruses. Together, this comprehensive analysis of viral HFs provides insights into the neglected role of viral integration in the evolution of amphioxus. [ABSTRACT FROM AUTHOR]

The annotated type list of Thamnophilidae (antbirds) in the Natural History Museum Vienna (NHMW) bird collection covers 52 taxa including 32 valid species, 18 subspecies and two taxa that are the basis of replacement names (nomina nova). 42 taxa are based on syntypes (including one uncertain case), eight on holotypes and one on paratypes. Among these, a majority is based on specimens collected by Johann Natterer from Brazil. Taxa represented by single specimens were collected by Friedrich Sellow, Wilhelm Hoffmanns, Henry George Watkins, Casimir Watkins, and George Flemming, respectively. Taxa and corresponding specimens, known to have been exchanged with or received from other institutions, are also documented. [ABSTRACT FROM AUTHOR]

Within phylum Chordata, the subphylum Cephalochordata (amphioxus and lancelets) has figured large in considerations of the evolutionary origin of the vertebrates. To date, these discussions have been predominantly based on knowledge of a single cephalochordate genus (Branchiostoma), almost to the exclusion of the other two genera (Asymmetron and Epigonichthys). This uneven pattern is illustrated by cephalochordate hematology, until now known entirely from work done on Branchiostoma. The main part of the present study is to describe hemocytes in the dorsal aorta of a species of Asymmetron by serial block-face scanning electron microscopy. This technique, which demonstrates three-dimensional fine structure, showed that the hemocytes have a relatively uniform morphology characterized by an oval shape and scanty cytoplasm. Ancillary information is also included for Branchiostoma hemocytes, known from previous studies to have relatively abundant cytoplasm; our serial block-face scanning electron microscopy provides more comprehensive views of the highly variable shapes of these cells, which typically extend one or several pseudopodium-like protrusions. The marked difference in hemocyte morphology found between Asymmetron and Branchiostoma was unexpected and directs attention to investigating comparable cells in the genus Epigonichthys. A broader knowledge of the hemocytes in all three cephalochordate genera would provide more balanced insights into the evolution of vertebrate hematopoiesis. [ABSTRACT FROM AUTHOR]

Published studies and ten new unpublished records included herein reveal that approximately 174 species of endoparasites (helminths and protozoans) are known from 65 of 163 species of rodents that occupy the subterranean ecotope globally. Of those, 94 endoparasite species were originally described from these rodents. A total of 282 host-parasite associations are summarized from four major zoogeographic regions including Ethiopian, Palearctic/Oriental, Nearctic, and Neotropical. Thirty-four parasite records from the literature have been identified to only the level of the genus. In this summary, ten new records have been added, and the most current taxonomic status of each parasite species is noted. Interestingly, there are no data on endoparasites from more than 68% of described subterranean rodents, which indicates that discovery and documentation are at an early stage and must continue. [ABSTRACT FROM AUTHOR]

Cytogenetic and compositional studies considered fish genomes rather poor in guanine-cytosine content (GC%) because of a putative "sharp increase in genic GC% during the evolution of higher vertebrates". However, the available genomic data have not been exploited to confirm this viewpoint. In contrast, further misunderstandings in GC%, mostly of fish genomes, originated from a misapprehension of the current flood of data. Utilizing public databases, we calculated the GC% in animal genomes of three different, technically well-established fractions: DNA (entire genome), cDNA (complementary DNA), and cds (exons). Our results across chordates help set borders of GC% values that are still incorrect in literature and show: (i) fish in their immense diversity possess comparably GC-rich (or even GC-richer) genomes as higher vertebrates, and fish exons are GC-enriched among vertebrates; (ii) animal genomes generally show a GC-enrichment from the DNA, over cDNA, to the cds level (i.e., not only the higher vertebrates); (iii) fish and invertebrates show a broad(er) inter-quartile range in GC%, while avian and mammalian genomes are more constrained in their GC%. These results indicate no sharp increase in the GC% of genes during the transition to higher vertebrates, as stated and numerously repeated before. We present our results in 2D and 3D space to explore the compositional genome landscape and prepared an online platform to explore the AT/GC compositional genome evolution. [ABSTRACT FROM AUTHOR]

This paper addresses a recent claim by Miyashita and co-authors that the filter-feeding larval lamprey is a new evolutionary addition to the lamprey life-cycle and does not provide information about early vertebrates, in contrast to the traditional view that this ammocoete stage resembles the first vertebrates. The evidence behind this revolutionary claim comes from fossil lampreys from 360–306 Mya that include young stages – even yolk-sac hatchlings – with adult (predacious) feeding structures. However, the traditional view is not so easily dismissed. The phylogeny on which the non-ammocoete theory is based was not tested in a statistically meaningful way. Additionally, the target article did not consider the known evidence for the traditional view, namely that the complex filter-feeding structures are highly similar in ammocoetes and the invertebrate chordates, amphioxus and tunicates. In further support of the traditional view, I show that ammocoetes are helpful for reconstructing the first vertebrates and the jawless, fossil stem gnathostomes called ostracoderms – their pharynx, oral cavity, mouth opening, lips and filter-feeding mode (but, ironically, not their mandibular/jaw region). From these considerations, I offer a scenario for the evolution of vertebrate life-cycles that fits the traditional, ammocoete-informed theory and puts filter feeding at centre stage. [ABSTRACT FROM AUTHOR]

Deuterostomes are the major division of animal life which includes sea stars, acorn worms, and humans, among a wide variety of ecologically and morphologically disparate taxa. However, their early evolution is poorly understood, due in part to their disparity, which makes identifying commonalities difficult, as well as their relatively poor early fossil record. Here, we review the available morphological, palaeontological, developmental, and molecular data to establish a framework for exploring the origins of this important and enigmatic group. Recent fossil discoveries strongly support a vermiform ancestor to the group Hemichordata, and a fusiform active swimmer as ancestor to Chordata. The diverse and anatomically bewildering variety of forms among the early echinoderms show evidence of both bilateral and radial symmetry. We consider four characteristics most critical for understanding the form and function of the last common ancestor to Deuterostomia: Hox gene expression patterns, larval morphology, the capacity for biomineralization, and the morphology of the pharyngeal region. We posit a deuterostome last common ancestor with a similar antero‐posterior gene regulatory system to that found in modern acorn worms and cephalochordates, a simple planktonic larval form, which was later elaborated in the ambulacrarian lineage, the ability to secrete calcium minerals in a limited fashion, and a pharyngeal respiratory region composed of simple pores. This animal was likely to be motile in adult form, as opposed to the sessile origins that have been historically suggested. Recent debates regarding deuterostome monophyly as well as the wide array of deuterostome‐affiliated problematica further suggest the possibility that those features were not only present in the last common ancestor of Deuterostomia, but potentially in the ur‐bilaterian. The morphology and development of the early deuterostomes, therefore, underpin some of the most significant questions in the study of metazoan evolution. [ABSTRACT FROM AUTHOR]

Asymmetries are essential for proper organization and function of organ systems. Genetic studies in bilaterians have shown signaling through the Nodal/Smad2 pathway plays a key, conserved role in the establishment of body asymmetries. Although the main molecular players in the network for the establishment of left-right asymmetry (LRA) have been deeply described in deuterostomes, little is known about the regulation of Nodal signaling in spiralians. Here, we identified orthologs of the egf-cfc gene, a master regulator of the Nodal pathway in vertebrates, in several invertebrate species, which includes the first evidence of its presence in non-deuterostomes. Our functional experiments indicate that despite being present, egf-cfc does not play a role in the establishment of LRA in gastropods. However, experiments in zebrafish suggest that a single amino acid mutation in the egf-cfc gene in at least the common ancestor of chordates was the necessary step to induce a gain of function in LRA regulation. This study shows that the egf-cfc gene likely appeared in the ancestors of deuterostomes and "protostomes", before being adopted as a mechanism to regulate the Nodal pathway and the establishment of LRA in some lineages of deuterostomes. [ABSTRACT FROM AUTHOR]

At least two of the six methionine (Met) residues in dehaloperoxidase (DHP) are shown to act as electron donors in both autoreduction and protein-heme crosslinking. Autoreduction observed in the two isozymes, DHP-A and DHP-B, is explained by the high heme reduction potential and an endogenous source of electrons from methionine (Met) or cysteine (Cys). This study provides evidence of a connection to protein-heme crosslinking that occurs when DHP is activated by H 2 O 2 in competition with substrate oxidation and autoreduction. The autoreduction yields of DHP-A and DHP-B are comparable and both are inversely proportional to DHP concentration. Both isoenzymes show an anti-cooperative effect on autoreduction kinetics associated with protein dimerization. Despite the presence of five tyrosine (Tyr) amino acids in DHP-A and four Tyr in DHP-B, the mass spectral evidence does not support a Tyr-heme or interprotein Tyr-Tyr crosslinking event as observed in some mammalian myoglobins. LC-MS and tandem MS/MS studies revealed three amino acids that were involved in the heme-protein crosslink, Cys73, Met63 and Met64. Cys73 facilitates dimer formation in DHP-A which also appears to slow the rate of autoreduction, but is not involved in covalent protein-heme crosslinking. Based on mutational studies, Met63 and 64 are involved in both covalent heme crosslinking and autoreduction. Proton-coupled electron transfer and crosslinking by Met to the heme may serve to regulate DHP function and protect it from uncontrolled oxidative damage. [Display omitted] • Autoreduction involves internal electron transfer from methionines and possibly cysteine. • Mass spectrometry shows role of methionine and cysteine in heme crosslinking. • The autoreduction yield is similar and anti-cooperative in both dehaloperoxidase-A and -B • Substrate binding in the distal pocket of the heme inhibits autoreduction. • The prevalence of methionine is high in annelids and mollusks but low in chordata. [ABSTRACT FROM AUTHOR]

Amphibians are facing population declines and extinctions, and protecting and supplementing refuges can help species survive. However, the microhabitat requirements of most species are unknown, and artificial shelters or burrows have not been well tested for amphibians. Some amphibians exhibit complex behaviour during the transition from post-reproductive dormancy to activity. However, little is known about the ecology, post-reproductive dormancy, and terrestrial activity of amphibians. Here, habitat site selection in experimental enclosures and the effects of shelters (stones, soil) and shade (with and without shade netting) on the activity, exposed body percentage, burrow depth, body-soil contact percentage, and survival of Rana dybowskii were investigated during post-reproductive dormancy and post-dormant activity. The results showed that R. dybowskii live individually under leaves, soil, stones or tree roots. Furthermore, although the dormant sites of frogs are significantly different, the distribution of male and female frogs in these sites is similar. Shading and shelter significantly affected the exposed body percentage, burrow depth and body-soil contact percentage of frogs compared with soil. In the stone group, soil and stone form the frog's refuge/burrow, whereas in the soil group, the refuge/burrow is composed entirely of soil. Even though the soil group has a deeper burrow and a larger area of soil contact with the body, it still has a higher exposure rate than the stone group. Frog activity frequency was affected by shelter and shade; the interaction of shelter and time and the interaction of shading and time were significant. The soil group had a higher activity frequency than the stone group, and the no-shade group had a higher activity frequency than the shade group. Shelter and shading differences do not significantly affect frog survival; however, the death rate during post-reproductive dormancy is lower than that during the active period. [ABSTRACT FROM AUTHOR]

The core molecular mechanisms of dorsal organizer formation during gastrulation are highly conserved within the chordate lineage. One of the key characteristics is that Nodal signaling is required for the organizer-specific gene expression. This feature appears to be ancestral, as evidenced by the presence in the most basally divergent chordate amphioxus. To provide a better understanding of the evolution of organizer-specific gene regulation in chordates, we analyzed the cis-regulatory sequence of amphioxus Chordin in the context of the vertebrate embryo. First, we generated stable zebrafish transgenic lines, and by using light-sheet fluorescent microscopy, characterized in detail the expression pattern of GFP driven by the cis-regulatory sequences of amphioxus Chordin. Next, we performed a 5′deletion analysis and identified an enhancer sufficient to drive the expression of the reporter gene into a chordate dorsal organizer. Finally, we found that the identified enhancer element strongly depends on Nodal signaling, which is consistent with the well-established role of this pathway in the regulation of the expression of dorsal organizer–specific genes across chordates. The enhancer identified in our study may represent a suitable simple system to study the interplay of the evolutionarily conserved regulatory mechanisms operating during early chordate development. [ABSTRACT FROM AUTHOR]

Incorporating measures of taxonomic diversity into research and management plans has long been a tenet of conservation science. Increasingly, active conservation programs are turning toward multispecies landscape and regional conservation actions, and away from single species approaches. This is both a reflection of changing trends in conservation science and advances in foundational technologies, including genomics and geospatial science. Multispecies approaches may provide more fundamental insights into evolutionary processes and equip managers with a more holistic understanding of the landscapes under their jurisdiction. Central to this approach are data generation and analyses which embrace and reflect a broad range of taxonomic diversity. Here, we examine the family-level phylogenetic breadth of the California Conservation Genomics Project (CCGP) based on family-level phylogenetic diversity (PD), family-level phylogenetic distinctness, and family richness. We place this in the context of the diversity present in California and compare it to the 35-plus years of genetic research compiled in the CaliPopGen Database. We found that the family-level PD in the CCGP reflected that of California very well, slightly overrepresenting chordates and underrepresenting arthropods, and that 42% of CCGP PD represented new contributions to genetic data for the state. In one focused effort, the CCGP was able to achieve roughly half the family-level PD studied over the last several decades. To maximize studied PD, future work should focus on arthropods, a conclusion that likely reflects the overall lack of attention to this hyperdiverse clade. [ABSTRACT FROM AUTHOR]

Aim: Reproductive output features prominently in many trait databases, but the metrics describing it vary and are often untethered to temporal and volumetric dimensions (e.g., fecundity per bout). The use of such ambiguous reproductive measures to make broad‐scale comparisons across taxonomic groups will be meaningful only if they show a 1:1 relationship with a reproductive measure that explicitly includes both a volumetric and a temporal component (i.e., reproductive mass per year). We sought to map the prevalence of ambiguous and explicit reproductive measures across taxa and to explore their relationships with one another to determine the cross‐compatibility and utility of reproductive metrics in trait databases. Location: Global. Time period: 1990–2021. Major taxa studied: We searched for reproductive measures across all Metazoa and identified 19,785 vertebrate species (Chordata), and 440 invertebrate species (Arthropoda, Cnidaria or Mollusca). Methods: We included 37 databases, from which we summarized the commonality of reproductive metrics across taxonomic groups. We also quantified scaling relationships between ambiguous reproductive traits (fecundity per bout, fecundity per year and reproductive mass per bout) and an explicit measure (reproductive mass per year) to assess their cross‐compatibility. Results: Most species were missing at least one temporal or volumetric dimension of reproductive output, such that reproductive mass per year could be reconstructed for only 4,786 vertebrate species. Ambiguous reproductive measures were poor predictors of reproductive mass per year; in no instance did these measures scale at 1:1. Main conclusions: Ambiguous measures systematically misestimate reproductive mass per year. Until more data are collected, we suggest that researchers should use the clade‐specific scaling relationships provided here to convert ambiguous reproductive measures to reproductive mass per year. [ABSTRACT FROM AUTHOR]

Global shipping facilitates the introduction of fouling organisms to new geographic areas. The increase in maritime transport in recent decades has led to unprecedented development, where marine coastal waters have become one of the most invaded habitats around the globe. Among the most successful invaders are ascidians. Despite the geographic and oceanographic isolation of Iceland, it is far from being excluded as a recipient region. Ascidians have successfully been able to establish stable populations in Iceland that are slowly expanding around the SW region. Here we report the first record of Ascidiella scabra in Icelandic waters, and the spread of seven non-indigenous ascidians across the S-SW Icelandic harbours. We compare their relative abundances to our survey from 2018. The bulk of these ascidians is not only present in the temperate Atlantic Ocean, but also in the Northwest Pacific and temperate Australasia, revealing that global homogenization of the ascidiofauna is emerging in anthropized coastal areas. The rising of sea surface temperature, driven by climate change, is likely to continue to support the development of this scenario leading to biodiversity loss, which could endanger living resources with severe economic impacts. [ABSTRACT FROM AUTHOR]